The 2nd Tsuchikage, Third Raikage, 2nd Mizukage & Fourth Kazekage were all planned as playable characters, but were excluded from the roster in the finished game. They are all still accessible through cheat devices, but were never completely finished.

Before the game came out, President Hiroshi Matsuyama was asked in an interview about "jutsu clashing", which had been removed in Naruto Shippuden: Ultimate Ninja Storm 2.

He said "Jutsu clashing using the repetition of the O button can be seen in the free battles of Storm 1 is not available in this game, but the jutsu clashing using button inputs that can be seen in the single player boss battles of Storm 2 exist in this new installment."

Two of the alternative costumes available for Naruto Uzumaki, a samurai outfit and Goku's uniform were based on illustrations by Masashi Kishimoto published in a Shonen Jump issue and an artbook. The two of them attracted producer Yuki Nishikawa who consulted other members from the company in order to include them in the game.

In August 2012, CyberConnect2 started a new suggestion forum in their official website, requesting players from all over the world to share their opinions regarding what they would like to see in Ultimate Ninja Storm 3 and upcoming Naruto games they would release. The feedback was used as a reference in creating the game.